--- _id: '9811' abstract: - lang: eng text: This document contains additional supporting evidence presented as supplemental tables. (XLSX 50Â kb) article_processing_charge: No author: - first_name: Luis full_name: Zapata, Luis last_name: Zapata - first_name: Oriol full_name: Pich, Oriol last_name: Pich - first_name: Luis full_name: Serrano, Luis last_name: Serrano - first_name: Fyodor full_name: Kondrashov, Fyodor id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 - first_name: Stephan full_name: Ossowski, Stephan last_name: Ossowski - first_name: Martin full_name: Schaefer, Martin last_name: Schaefer citation: ama: 'Zapata L, Pich O, Serrano L, Kondrashov F, Ossowski S, Schaefer M. Additional file 1: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome. 2018. doi:10.6084/m9.figshare.6401390.v1' apa: 'Zapata, L., Pich, O., Serrano, L., Kondrashov, F., Ossowski, S., & Schaefer, M. (2018). Additional file 1: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome. Springer Nature. https://doi.org/10.6084/m9.figshare.6401390.v1' chicago: 'Zapata, Luis, Oriol Pich, Luis Serrano, Fyodor Kondrashov, Stephan Ossowski, and Martin Schaefer. “Additional File 1: Of Negative Selection in Tumor Genome Evolution Acts on Essential Cellular Functions and the Immunopeptidome.” Springer Nature, 2018. https://doi.org/10.6084/m9.figshare.6401390.v1.' ieee: 'L. Zapata, O. Pich, L. Serrano, F. Kondrashov, S. Ossowski, and M. Schaefer, “Additional file 1: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome.” Springer Nature, 2018.' ista: 'Zapata L, Pich O, Serrano L, Kondrashov F, Ossowski S, Schaefer M. 2018. Additional file 1: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome, Springer Nature, 10.6084/m9.figshare.6401390.v1.' mla: 'Zapata, Luis, et al. Additional File 1: Of Negative Selection in Tumor Genome Evolution Acts on Essential Cellular Functions and the Immunopeptidome. Springer Nature, 2018, doi:10.6084/m9.figshare.6401390.v1.' short: L. Zapata, O. Pich, L. Serrano, F. Kondrashov, S. Ossowski, M. Schaefer, (2018). date_created: 2021-08-06T12:53:49Z date_published: 2018-05-31T00:00:00Z date_updated: 2023-09-13T09:01:31Z day: '31' department: - _id: FyKo doi: 10.6084/m9.figshare.6401390.v1 main_file_link: - open_access: '1' url: https://doi.org/10.6084/m9.figshare.6401390.v1 month: '05' oa: 1 oa_version: Preprint publisher: Springer Nature related_material: record: - id: '279' relation: used_in_publication status: public status: public title: 'Additional file 1: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome' type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2018' ... --- _id: '20' abstract: - lang: eng text: 'Background: Norepinephrine (NE) signaling has a key role in white adipose tissue (WAT) functions, including lipolysis, free fatty acid liberation and, under certain conditions, conversion of white into brite (brown-in-white) adipocytes. However, acute effects of NE stimulation have not been described at the transcriptional network level. Results: We used RNA-seq to uncover a broad transcriptional response. The inference of protein-protein and protein-DNA interaction networks allowed us to identify a set of immediate-early genes (IEGs) with high betweenness, validating our approach and suggesting a hierarchical control of transcriptional regulation. In addition, we identified a transcriptional regulatory network with IEGs as master regulators, including HSF1 and NFIL3 as novel NE-induced IEG candidates. Moreover, a functional enrichment analysis and gene clustering into functional modules suggest a crosstalk between metabolic, signaling, and immune responses. Conclusions: Altogether, our network biology approach explores for the first time the immediate-early systems level response of human adipocytes to acute sympathetic activation, thereby providing a first network basis of early cell fate programs and crosstalks between metabolic and transcriptional networks required for proper WAT function.' acknowledgement: This work was funded by the German Centre for Diabetes Research (DZD) and the Austrian Science Fund (FWF, P25729-B19). article_processing_charge: No article_type: original author: - first_name: Juan full_name: Higareda Almaraz, Juan last_name: Higareda Almaraz - first_name: Michael full_name: Karbiener, Michael last_name: Karbiener - first_name: Maude full_name: Giroud, Maude last_name: Giroud - first_name: Florian full_name: Pauler, Florian id: 48EA0138-F248-11E8-B48F-1D18A9856A87 last_name: Pauler orcid: 0000-0002-7462-0048 - first_name: Teresa full_name: Gerhalter, Teresa last_name: Gerhalter - first_name: Stephan full_name: Herzig, Stephan last_name: Herzig - first_name: Marcel full_name: Scheideler, Marcel last_name: Scheideler citation: ama: Higareda Almaraz J, Karbiener M, Giroud M, et al. Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes. BMC Genomics. 2018;19(1). doi:10.1186/s12864-018-5173-0 apa: Higareda Almaraz, J., Karbiener, M., Giroud, M., Pauler, F., Gerhalter, T., Herzig, S., & Scheideler, M. (2018). Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes. BMC Genomics. BioMed Central. https://doi.org/10.1186/s12864-018-5173-0 chicago: Higareda Almaraz, Juan, Michael Karbiener, Maude Giroud, Florian Pauler, Teresa Gerhalter, Stephan Herzig, and Marcel Scheideler. “Norepinephrine Triggers an Immediate-Early Regulatory Network Response in Primary Human White Adipocytes.” BMC Genomics. BioMed Central, 2018. https://doi.org/10.1186/s12864-018-5173-0. ieee: J. Higareda Almaraz et al., “Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes,” BMC Genomics, vol. 19, no. 1. BioMed Central, 2018. ista: Higareda Almaraz J, Karbiener M, Giroud M, Pauler F, Gerhalter T, Herzig S, Scheideler M. 2018. Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes. BMC Genomics. 19(1). mla: Higareda Almaraz, Juan, et al. “Norepinephrine Triggers an Immediate-Early Regulatory Network Response in Primary Human White Adipocytes.” BMC Genomics, vol. 19, no. 1, BioMed Central, 2018, doi:10.1186/s12864-018-5173-0. short: J. Higareda Almaraz, M. Karbiener, M. Giroud, F. Pauler, T. Gerhalter, S. Herzig, M. Scheideler, BMC Genomics 19 (2018). date_created: 2018-12-11T11:44:12Z date_published: 2018-11-03T00:00:00Z date_updated: 2023-09-13T09:10:47Z day: '03' ddc: - '570' department: - _id: SiHi doi: 10.1186/s12864-018-5173-0 external_id: isi: - '000450976700002' file: - access_level: open_access checksum: a56516e734dab589dc7f3e1915973b4d content_type: application/pdf creator: dernst date_created: 2018-12-17T14:52:57Z date_updated: 2020-07-14T12:45:23Z file_id: '5712' file_name: 2018_BMCGenomics_Higareda.pdf file_size: 4629784 relation: main_file file_date_updated: 2020-07-14T12:45:23Z has_accepted_license: '1' intvolume: ' 19' isi: 1 issue: '1' language: - iso: eng month: '11' oa: 1 oa_version: Published Version publication: BMC Genomics publication_identifier: issn: - 1471-2164 publication_status: published publisher: BioMed Central publist_id: '8035' quality_controlled: '1' related_material: record: - id: '9807' relation: research_data status: public - id: '9808' relation: research_data status: public scopus_import: '1' status: public title: Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 19 year: '2018' ... --- _id: '107' abstract: - lang: eng text: 'We introduce the notion of “non-malleable codes” which relaxes the notion of error correction and error detection. Informally, a code is non-malleable if the message contained in a modified codeword is either the original message, or a completely unrelated value. In contrast to error correction and error detection, non-malleability can be achieved for very rich classes of modifications. We construct an efficient code that is non-malleable with respect to modifications that affect each bit of the codeword arbitrarily (i.e., leave it untouched, flip it, or set it to either 0 or 1), but independently of the value of the other bits of the codeword. Using the probabilistic method, we also show a very strong and general statement: there exists a non-malleable code for every “small enough” family F of functions via which codewords can be modified. Although this probabilistic method argument does not directly yield efficient constructions, it gives us efficient non-malleable codes in the random-oracle model for very general classes of tampering functions—e.g., functions where every bit in the tampered codeword can depend arbitrarily on any 99% of the bits in the original codeword. As an application of non-malleable codes, we show that they provide an elegant algorithmic solution to the task of protecting functionalities implemented in hardware (e.g., signature cards) against “tampering attacks.” In such attacks, the secret state of a physical system is tampered, in the hopes that future interaction with the modified system will reveal some secret information. This problem was previously studied in the work of Gennaro et al. in 2004 under the name “algorithmic tamper proof security” (ATP). We show that non-malleable codes can be used to achieve important improvements over the prior work. In particular, we show that any functionality can be made secure against a large class of tampering attacks, simply by encoding the secret state with a non-malleable code while it is stored in memory.' article_number: '20' article_processing_charge: No article_type: original author: - first_name: Stefan full_name: Dziembowski, Stefan last_name: Dziembowski - first_name: Krzysztof Z full_name: Pietrzak, Krzysztof Z id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87 last_name: Pietrzak orcid: 0000-0002-9139-1654 - first_name: Daniel full_name: Wichs, Daniel last_name: Wichs citation: ama: Dziembowski S, Pietrzak KZ, Wichs D. Non-malleable codes. Journal of the ACM. 2018;65(4). doi:10.1145/3178432 apa: Dziembowski, S., Pietrzak, K. Z., & Wichs, D. (2018). Non-malleable codes. Journal of the ACM. ACM. https://doi.org/10.1145/3178432 chicago: Dziembowski, Stefan, Krzysztof Z Pietrzak, and Daniel Wichs. “Non-Malleable Codes.” Journal of the ACM. ACM, 2018. https://doi.org/10.1145/3178432. ieee: S. Dziembowski, K. Z. Pietrzak, and D. Wichs, “Non-malleable codes,” Journal of the ACM, vol. 65, no. 4. ACM, 2018. ista: Dziembowski S, Pietrzak KZ, Wichs D. 2018. Non-malleable codes. Journal of the ACM. 65(4), 20. mla: Dziembowski, Stefan, et al. “Non-Malleable Codes.” Journal of the ACM, vol. 65, no. 4, 20, ACM, 2018, doi:10.1145/3178432. short: S. Dziembowski, K.Z. Pietrzak, D. Wichs, Journal of the ACM 65 (2018). date_created: 2018-12-11T11:44:40Z date_published: 2018-08-01T00:00:00Z date_updated: 2023-09-13T09:05:17Z day: '01' department: - _id: KrPi doi: 10.1145/3178432 ec_funded: 1 external_id: isi: - '000442938200004' intvolume: ' 65' isi: 1 issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: https://eprint.iacr.org/2009/608 month: '08' oa: 1 oa_version: Preprint project: - _id: 258AA5B2-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '682815' name: Teaching Old Crypto New Tricks - _id: 258C570E-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '259668' name: Provable Security for Physical Cryptography publication: Journal of the ACM publication_status: published publisher: ACM publist_id: '7947' quality_controlled: '1' scopus_import: '1' status: public title: Non-malleable codes type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 65 year: '2018' ... --- _id: '5676' abstract: - lang: eng text: 'In epithelial tissues, cells tightly connect to each other through cell–cell junctions, but they also present the remarkable capacity of reorganizing themselves without compromising tissue integrity. Upon injury, simple epithelia efficiently resolve small lesions through the action of actin cytoskeleton contractile structures at the wound edge and cellular rearrangements. However, the underlying mechanisms and how they cooperate are still poorly understood. In this study, we combine live imaging and theoretical modeling to reveal a novel and indispensable role for occluding junctions (OJs) in this process. We demonstrate that OJ loss of function leads to defects in wound-closure dynamics: instead of contracting, wounds dramatically increase their area. OJ mutants exhibit phenotypes in cell shape, cellular rearrangements, and mechanical properties as well as in actin cytoskeleton dynamics at the wound edge. We propose that OJs are essential for wound closure by impacting on epithelial mechanics at the tissue level, which in turn is crucial for correct regulation of the cellular events occurring at the wound edge.' article_processing_charge: No author: - first_name: Lara full_name: Carvalho, Lara last_name: Carvalho - first_name: Pedro full_name: Patricio, Pedro last_name: Patricio - first_name: Susana full_name: Ponte, Susana last_name: Ponte - first_name: Carl-Philipp J full_name: Heisenberg, Carl-Philipp J id: 39427864-F248-11E8-B48F-1D18A9856A87 last_name: Heisenberg orcid: 0000-0002-0912-4566 - first_name: Luis full_name: Almeida, Luis last_name: Almeida - first_name: André S. full_name: Nunes, André S. last_name: Nunes - first_name: Nuno A.M. full_name: Araújo, Nuno A.M. last_name: Araújo - first_name: Antonio full_name: Jacinto, Antonio last_name: Jacinto citation: ama: Carvalho L, Patricio P, Ponte S, et al. Occluding junctions as novel regulators of tissue mechanics during wound repair. Journal of Cell Biology. 2018;217(12):4267-4283. doi:10.1083/jcb.201804048 apa: Carvalho, L., Patricio, P., Ponte, S., Heisenberg, C.-P. J., Almeida, L., Nunes, A. S., … Jacinto, A. (2018). Occluding junctions as novel regulators of tissue mechanics during wound repair. Journal of Cell Biology. Rockefeller University Press. https://doi.org/10.1083/jcb.201804048 chicago: Carvalho, Lara, Pedro Patricio, Susana Ponte, Carl-Philipp J Heisenberg, Luis Almeida, André S. Nunes, Nuno A.M. Araújo, and Antonio Jacinto. “Occluding Junctions as Novel Regulators of Tissue Mechanics during Wound Repair.” Journal of Cell Biology. Rockefeller University Press, 2018. https://doi.org/10.1083/jcb.201804048. ieee: L. Carvalho et al., “Occluding junctions as novel regulators of tissue mechanics during wound repair,” Journal of Cell Biology, vol. 217, no. 12. Rockefeller University Press, pp. 4267–4283, 2018. ista: Carvalho L, Patricio P, Ponte S, Heisenberg C-PJ, Almeida L, Nunes AS, Araújo NAM, Jacinto A. 2018. Occluding junctions as novel regulators of tissue mechanics during wound repair. Journal of Cell Biology. 217(12), 4267–4283. mla: Carvalho, Lara, et al. “Occluding Junctions as Novel Regulators of Tissue Mechanics during Wound Repair.” Journal of Cell Biology, vol. 217, no. 12, Rockefeller University Press, 2018, pp. 4267–83, doi:10.1083/jcb.201804048. short: L. Carvalho, P. Patricio, S. Ponte, C.-P.J. Heisenberg, L. Almeida, A.S. Nunes, N.A.M. Araújo, A. Jacinto, Journal of Cell Biology 217 (2018) 4267–4283. date_created: 2018-12-16T22:59:19Z date_published: 2018-12-01T00:00:00Z date_updated: 2023-09-13T09:11:17Z day: '01' department: - _id: CaHe doi: 10.1083/jcb.201804048 ec_funded: 1 external_id: isi: - '000451960800018' pmid: - '30228162 ' intvolume: ' 217' isi: 1 issue: '12' language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pubmed/30228162 month: '12' oa: 1 oa_version: Submitted Version page: 4267-4283 pmid: 1 project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: Journal of Cell Biology publication_identifier: issn: - '00219525' publication_status: published publisher: Rockefeller University Press quality_controlled: '1' scopus_import: '1' status: public title: Occluding junctions as novel regulators of tissue mechanics during wound repair type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 217 year: '2018' ... --- _id: '9807' abstract: - lang: eng text: Table S1. Genes with highest betweenness. Table S2. Local and Master regulators up-regulated. Table S3. Local and Master regulators down-regulated (XLSX 23 kb). article_processing_charge: No author: - first_name: Juan full_name: Higareda Almaraz, Juan last_name: Higareda Almaraz - first_name: Michael full_name: Karbiener, Michael last_name: Karbiener - first_name: Maude full_name: Giroud, Maude last_name: Giroud - first_name: Florian full_name: Pauler, Florian id: 48EA0138-F248-11E8-B48F-1D18A9856A87 last_name: Pauler orcid: 0000-0002-7462-0048 - first_name: Teresa full_name: Gerhalter, Teresa last_name: Gerhalter - first_name: Stephan full_name: Herzig, Stephan last_name: Herzig - first_name: Marcel full_name: Scheideler, Marcel last_name: Scheideler citation: ama: 'Higareda Almaraz J, Karbiener M, Giroud M, et al. Additional file 1: Of Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes. 2018. doi:10.6084/m9.figshare.7295339.v1' apa: 'Higareda Almaraz, J., Karbiener, M., Giroud, M., Pauler, F., Gerhalter, T., Herzig, S., & Scheideler, M. (2018). Additional file 1: Of Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes. Springer Nature. https://doi.org/10.6084/m9.figshare.7295339.v1' chicago: 'Higareda Almaraz, Juan, Michael Karbiener, Maude Giroud, Florian Pauler, Teresa Gerhalter, Stephan Herzig, and Marcel Scheideler. “Additional File 1: Of Norepinephrine Triggers an Immediate-Early Regulatory Network Response in Primary Human White Adipocytes.” Springer Nature, 2018. https://doi.org/10.6084/m9.figshare.7295339.v1.' ieee: 'J. Higareda Almaraz et al., “Additional file 1: Of Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes.” Springer Nature, 2018.' ista: 'Higareda Almaraz J, Karbiener M, Giroud M, Pauler F, Gerhalter T, Herzig S, Scheideler M. 2018. Additional file 1: Of Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes, Springer Nature, 10.6084/m9.figshare.7295339.v1.' mla: 'Higareda Almaraz, Juan, et al. Additional File 1: Of Norepinephrine Triggers an Immediate-Early Regulatory Network Response in Primary Human White Adipocytes. Springer Nature, 2018, doi:10.6084/m9.figshare.7295339.v1.' short: J. Higareda Almaraz, M. Karbiener, M. Giroud, F. Pauler, T. Gerhalter, S. Herzig, M. Scheideler, (2018). date_created: 2021-08-06T12:26:53Z date_published: 2018-11-03T00:00:00Z date_updated: 2023-09-13T09:10:47Z day: '03' department: - _id: SiHi doi: 10.6084/m9.figshare.7295339.v1 main_file_link: - open_access: '1' url: https://doi.org/10.6084/m9.figshare.7295339.v1 month: '11' oa: 1 oa_version: Published Version publisher: Springer Nature related_material: record: - id: '20' relation: used_in_publication status: public status: public title: 'Additional file 1: Of Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes' type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2018' ... --- _id: '9808' abstract: - lang: eng text: Table S4. Counts per Gene per Million Reads Mapped. (XLSX 2751 kb). article_processing_charge: No author: - first_name: Juan full_name: Higareda Almaraz, Juan last_name: Higareda Almaraz - first_name: Michael full_name: Karbiener, Michael last_name: Karbiener - first_name: Maude full_name: Giroud, Maude last_name: Giroud - first_name: Florian full_name: Pauler, Florian id: 48EA0138-F248-11E8-B48F-1D18A9856A87 last_name: Pauler orcid: 0000-0002-7462-0048 - first_name: Teresa full_name: Gerhalter, Teresa last_name: Gerhalter - first_name: Stephan full_name: Herzig, Stephan last_name: Herzig - first_name: Marcel full_name: Scheideler, Marcel last_name: Scheideler citation: ama: 'Higareda Almaraz J, Karbiener M, Giroud M, et al. Additional file 3: Of Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes. 2018. doi:10.6084/m9.figshare.7295369.v1' apa: 'Higareda Almaraz, J., Karbiener, M., Giroud, M., Pauler, F., Gerhalter, T., Herzig, S., & Scheideler, M. (2018). Additional file 3: Of Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes. Springer Nature. https://doi.org/10.6084/m9.figshare.7295369.v1' chicago: 'Higareda Almaraz, Juan, Michael Karbiener, Maude Giroud, Florian Pauler, Teresa Gerhalter, Stephan Herzig, and Marcel Scheideler. “Additional File 3: Of Norepinephrine Triggers an Immediate-Early Regulatory Network Response in Primary Human White Adipocytes.” Springer Nature, 2018. https://doi.org/10.6084/m9.figshare.7295369.v1.' ieee: 'J. Higareda Almaraz et al., “Additional file 3: Of Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes.” Springer Nature, 2018.' ista: 'Higareda Almaraz J, Karbiener M, Giroud M, Pauler F, Gerhalter T, Herzig S, Scheideler M. 2018. Additional file 3: Of Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes, Springer Nature, 10.6084/m9.figshare.7295369.v1.' mla: 'Higareda Almaraz, Juan, et al. Additional File 3: Of Norepinephrine Triggers an Immediate-Early Regulatory Network Response in Primary Human White Adipocytes. Springer Nature, 2018, doi:10.6084/m9.figshare.7295369.v1.' short: J. Higareda Almaraz, M. Karbiener, M. Giroud, F. Pauler, T. Gerhalter, S. Herzig, M. Scheideler, (2018). date_created: 2021-08-06T12:31:57Z date_published: 2018-11-03T00:00:00Z date_updated: 2023-09-13T09:10:47Z day: '03' department: - _id: SiHi doi: 10.6084/m9.figshare.7295369.v1 main_file_link: - open_access: '1' url: https://doi.org/10.6084/m9.figshare.7295369.v1 month: '11' oa: 1 oa_version: Published Version publisher: Springer Nature related_material: record: - id: '20' relation: used_in_publication status: public status: public title: 'Additional file 3: Of Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes' type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2018' ... --- _id: '193' abstract: - lang: eng text: 'We show attacks on five data-independent memory-hard functions (iMHF) that were submitted to the password hashing competition (PHC). Informally, an MHF is a function which cannot be evaluated on dedicated hardware, like ASICs, at significantly lower hardware and/or energy cost than evaluating a single instance on a standard single-core architecture. Data-independent means the memory access pattern of the function is independent of the input; this makes iMHFs harder to construct than data-dependent ones, but the latter can be attacked by various side-channel attacks. Following [Alwen-Blocki''16], we capture the evaluation of an iMHF as a directed acyclic graph (DAG). The cumulative parallel pebbling complexity of this DAG is a measure for the hardware cost of evaluating the iMHF on an ASIC. Ideally, one would like the complexity of a DAG underlying an iMHF to be as close to quadratic in the number of nodes of the graph as possible. Instead, we show that (the DAGs underlying) the following iMHFs are far from this bound: Rig.v2, TwoCats and Gambit each having an exponent no more than 1.75. Moreover, we show that the complexity of the iMHF modes of the PHC finalists Pomelo and Lyra2 have exponents at most 1.83 and 1.67 respectively. To show this we investigate a combinatorial property of each underlying DAG (called its depth-robustness. By establishing upper bounds on this property we are then able to apply the general technique of [Alwen-Block''16] for analyzing the hardware costs of an iMHF.' acknowledgement: Leonid Reyzin was supported in part by IST Austria and by US NSF grants 1012910, 1012798, and 1422965; this research was performed while he was visiting IST Austria. article_processing_charge: No author: - first_name: Joel F full_name: Alwen, Joel F id: 2A8DFA8C-F248-11E8-B48F-1D18A9856A87 last_name: Alwen - first_name: Peter full_name: Gazi, Peter last_name: Gazi - first_name: Chethan full_name: Kamath Hosdurg, Chethan id: 4BD3F30E-F248-11E8-B48F-1D18A9856A87 last_name: Kamath Hosdurg - first_name: Karen full_name: Klein, Karen id: 3E83A2F8-F248-11E8-B48F-1D18A9856A87 last_name: Klein - first_name: Georg F full_name: Osang, Georg F id: 464B40D6-F248-11E8-B48F-1D18A9856A87 last_name: Osang orcid: 0000-0002-8882-5116 - first_name: Krzysztof Z full_name: Pietrzak, Krzysztof Z id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87 last_name: Pietrzak orcid: 0000-0002-9139-1654 - first_name: Lenoid full_name: Reyzin, Lenoid last_name: Reyzin - first_name: Michal full_name: Rolinek, Michal id: 3CB3BC06-F248-11E8-B48F-1D18A9856A87 last_name: Rolinek - first_name: Michal full_name: Rybar, Michal id: 2B3E3DE8-F248-11E8-B48F-1D18A9856A87 last_name: Rybar citation: ama: 'Alwen JF, Gazi P, Kamath Hosdurg C, et al. On the memory hardness of data independent password hashing functions. In: Proceedings of the 2018 on Asia Conference on Computer and Communication Security. ACM; 2018:51-65. doi:10.1145/3196494.3196534' apa: 'Alwen, J. F., Gazi, P., Kamath Hosdurg, C., Klein, K., Osang, G. F., Pietrzak, K. Z., … Rybar, M. (2018). On the memory hardness of data independent password hashing functions. In Proceedings of the 2018 on Asia Conference on Computer and Communication Security (pp. 51–65). Incheon, Republic of Korea: ACM. https://doi.org/10.1145/3196494.3196534' chicago: Alwen, Joel F, Peter Gazi, Chethan Kamath Hosdurg, Karen Klein, Georg F Osang, Krzysztof Z Pietrzak, Lenoid Reyzin, Michal Rolinek, and Michal Rybar. “On the Memory Hardness of Data Independent Password Hashing Functions.” In Proceedings of the 2018 on Asia Conference on Computer and Communication Security, 51–65. ACM, 2018. https://doi.org/10.1145/3196494.3196534. ieee: J. F. Alwen et al., “On the memory hardness of data independent password hashing functions,” in Proceedings of the 2018 on Asia Conference on Computer and Communication Security, Incheon, Republic of Korea, 2018, pp. 51–65. ista: 'Alwen JF, Gazi P, Kamath Hosdurg C, Klein K, Osang GF, Pietrzak KZ, Reyzin L, Rolinek M, Rybar M. 2018. On the memory hardness of data independent password hashing functions. Proceedings of the 2018 on Asia Conference on Computer and Communication Security. ASIACCS: Asia Conference on Computer and Communications Security , 51–65.' mla: Alwen, Joel F., et al. “On the Memory Hardness of Data Independent Password Hashing Functions.” Proceedings of the 2018 on Asia Conference on Computer and Communication Security, ACM, 2018, pp. 51–65, doi:10.1145/3196494.3196534. short: J.F. Alwen, P. Gazi, C. Kamath Hosdurg, K. Klein, G.F. Osang, K.Z. Pietrzak, L. Reyzin, M. Rolinek, M. Rybar, in:, Proceedings of the 2018 on Asia Conference on Computer and Communication Security, ACM, 2018, pp. 51–65. conference: end_date: 2018-06-08 location: Incheon, Republic of Korea name: 'ASIACCS: Asia Conference on Computer and Communications Security ' start_date: 2018-06-04 date_created: 2018-12-11T11:45:07Z date_published: 2018-06-01T00:00:00Z date_updated: 2023-09-13T09:13:12Z day: '01' department: - _id: KrPi - _id: HeEd - _id: VlKo doi: 10.1145/3196494.3196534 ec_funded: 1 external_id: isi: - '000516620100005' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://eprint.iacr.org/2016/783 month: '06' oa: 1 oa_version: Submitted Version page: 51 - 65 project: - _id: 25FBA906-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '616160' name: 'Discrete Optimization in Computer Vision: Theory and Practice' - _id: 258AA5B2-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '682815' name: Teaching Old Crypto New Tricks publication: Proceedings of the 2018 on Asia Conference on Computer and Communication Security publication_status: published publisher: ACM publist_id: '7723' quality_controlled: '1' scopus_import: '1' status: public title: On the memory hardness of data independent password hashing functions type: conference user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2018' ... --- _id: '300' abstract: - lang: eng text: We introduce a formal quantitative notion of “bit security” for a general type of cryptographic games (capturing both decision and search problems), aimed at capturing the intuition that a cryptographic primitive with k-bit security is as hard to break as an ideal cryptographic function requiring a brute force attack on a k-bit key space. Our new definition matches the notion of bit security commonly used by cryptographers and cryptanalysts when studying search (e.g., key recovery) problems, where the use of the traditional definition is well established. However, it produces a quantitatively different metric in the case of decision (indistinguishability) problems, where the use of (a straightforward generalization of) the traditional definition is more problematic and leads to a number of paradoxical situations or mismatches between theoretical/provable security and practical/common sense intuition. Key to our new definition is to consider adversaries that may explicitly declare failure of the attack. We support and justify the new definition by proving a number of technical results, including tight reductions between several standard cryptographic problems, a new hybrid theorem that preserves bit security, and an application to the security analysis of indistinguishability primitives making use of (approximate) floating point numbers. This is the first result showing that (standard precision) 53-bit floating point numbers can be used to achieve 100-bit security in the context of cryptographic primitives with general indistinguishability-based security definitions. Previous results of this type applied only to search problems, or special types of decision problems. acknowledgement: Research supported in part by the Defense Advanced Research Projects Agency (DARPA) and the U.S. Army Research Office under the SafeWare program. Opinions, findings and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views, position or policy of the Government. The second author was also supported by the European Research Council, ERC consolidator grant (682815 - TOCNeT). alternative_title: - LNCS article_processing_charge: No author: - first_name: Daniele full_name: Micciancio, Daniele last_name: Micciancio - first_name: Michael full_name: Walter, Michael id: 488F98B0-F248-11E8-B48F-1D18A9856A87 last_name: Walter orcid: 0000-0003-3186-2482 citation: ama: 'Micciancio D, Walter M. On the bit security of cryptographic primitives. In: Vol 10820. Springer; 2018:3-28. doi:10.1007/978-3-319-78381-9_1' apa: 'Micciancio, D., & Walter, M. (2018). On the bit security of cryptographic primitives (Vol. 10820, pp. 3–28). Presented at the Eurocrypt: Advances in Cryptology, Tel Aviv, Israel: Springer. https://doi.org/10.1007/978-3-319-78381-9_1' chicago: Micciancio, Daniele, and Michael Walter. “On the Bit Security of Cryptographic Primitives,” 10820:3–28. Springer, 2018. https://doi.org/10.1007/978-3-319-78381-9_1. ieee: 'D. Micciancio and M. Walter, “On the bit security of cryptographic primitives,” presented at the Eurocrypt: Advances in Cryptology, Tel Aviv, Israel, 2018, vol. 10820, pp. 3–28.' ista: 'Micciancio D, Walter M. 2018. On the bit security of cryptographic primitives. Eurocrypt: Advances in Cryptology, LNCS, vol. 10820, 3–28.' mla: Micciancio, Daniele, and Michael Walter. On the Bit Security of Cryptographic Primitives. Vol. 10820, Springer, 2018, pp. 3–28, doi:10.1007/978-3-319-78381-9_1. short: D. Micciancio, M. Walter, in:, Springer, 2018, pp. 3–28. conference: end_date: 2018-05-03 location: Tel Aviv, Israel name: 'Eurocrypt: Advances in Cryptology' start_date: 2018-04-29 date_created: 2018-12-11T11:45:42Z date_published: 2018-03-31T00:00:00Z date_updated: 2023-09-13T09:12:04Z day: '31' department: - _id: KrPi doi: 10.1007/978-3-319-78381-9_1 ec_funded: 1 external_id: isi: - '000517097500001' intvolume: ' 10820' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://eprint.iacr.org/2018/077 month: '03' oa: 1 oa_version: Submitted Version page: 3 - 28 project: - _id: 258AA5B2-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '682815' name: Teaching Old Crypto New Tricks publication_status: published publisher: Springer publist_id: '7581' quality_controlled: '1' scopus_import: '1' status: public title: On the bit security of cryptographic primitives type: conference user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 10820 year: '2018' ... --- _id: '312' abstract: - lang: eng text: Motivated by biological questions, we study configurations of equal spheres that neither pack nor cover. Placing their centers on a lattice, we define the soft density of the configuration by penalizing multiple overlaps. Considering the 1-parameter family of diagonally distorted 3-dimensional integer lattices, we show that the soft density is maximized at the FCC lattice. acknowledgement: This work was partially supported by the DFG Collaborative Research Center TRR 109, “Discretization in Geometry and Dynamics,” through grant I02979-N35 of the Austrian Science Fund (FWF). article_processing_charge: No article_type: original author: - first_name: Herbert full_name: Edelsbrunner, Herbert id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 - first_name: Mabel full_name: Iglesias Ham, Mabel id: 41B58C0C-F248-11E8-B48F-1D18A9856A87 last_name: Iglesias Ham citation: ama: Edelsbrunner H, Iglesias Ham M. On the optimality of the FCC lattice for soft sphere packing. SIAM J Discrete Math. 2018;32(1):750-782. doi:10.1137/16M1097201 apa: Edelsbrunner, H., & Iglesias Ham, M. (2018). On the optimality of the FCC lattice for soft sphere packing. SIAM J Discrete Math. Society for Industrial and Applied Mathematics . https://doi.org/10.1137/16M1097201 chicago: Edelsbrunner, Herbert, and Mabel Iglesias Ham. “On the Optimality of the FCC Lattice for Soft Sphere Packing.” SIAM J Discrete Math. Society for Industrial and Applied Mathematics , 2018. https://doi.org/10.1137/16M1097201. ieee: H. Edelsbrunner and M. Iglesias Ham, “On the optimality of the FCC lattice for soft sphere packing,” SIAM J Discrete Math, vol. 32, no. 1. Society for Industrial and Applied Mathematics , pp. 750–782, 2018. ista: Edelsbrunner H, Iglesias Ham M. 2018. On the optimality of the FCC lattice for soft sphere packing. SIAM J Discrete Math. 32(1), 750–782. mla: Edelsbrunner, Herbert, and Mabel Iglesias Ham. “On the Optimality of the FCC Lattice for Soft Sphere Packing.” SIAM J Discrete Math, vol. 32, no. 1, Society for Industrial and Applied Mathematics , 2018, pp. 750–82, doi:10.1137/16M1097201. short: H. Edelsbrunner, M. Iglesias Ham, SIAM J Discrete Math 32 (2018) 750–782. date_created: 2018-12-11T11:45:46Z date_published: 2018-03-29T00:00:00Z date_updated: 2023-09-13T09:34:38Z day: '29' department: - _id: HeEd doi: 10.1137/16M1097201 external_id: isi: - '000428958900038' intvolume: ' 32' isi: 1 issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: http://pdfs.semanticscholar.org/d2d5/6da00fbc674e6a8b1bb9d857167e54200dc6.pdf month: '03' oa: 1 oa_version: Submitted Version page: 750 - 782 project: - _id: 2561EBF4-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: I02979-N35 name: Persistence and stability of geometric complexes publication: SIAM J Discrete Math publication_identifier: issn: - '08954801' publication_status: published publisher: 'Society for Industrial and Applied Mathematics ' publist_id: '7553' quality_controlled: '1' scopus_import: '1' status: public title: On the optimality of the FCC lattice for soft sphere packing type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 32 year: '2018' ... --- _id: '409' abstract: - lang: eng text: We give a simple proof of T. Stehling's result [4], whereby in any normal tiling of the plane with convex polygons with number of sides not less than six, all tiles except a finite number are hexagons. article_processing_charge: No article_type: original author: - first_name: Arseniy full_name: Akopyan, Arseniy id: 430D2C90-F248-11E8-B48F-1D18A9856A87 last_name: Akopyan orcid: 0000-0002-2548-617X citation: ama: Akopyan A. On the number of non-hexagons in a planar tiling. Comptes Rendus Mathematique. 2018;356(4):412-414. doi:10.1016/j.crma.2018.03.005 apa: Akopyan, A. (2018). On the number of non-hexagons in a planar tiling. Comptes Rendus Mathematique. Elsevier. https://doi.org/10.1016/j.crma.2018.03.005 chicago: Akopyan, Arseniy. “On the Number of Non-Hexagons in a Planar Tiling.” Comptes Rendus Mathematique. Elsevier, 2018. https://doi.org/10.1016/j.crma.2018.03.005. ieee: A. Akopyan, “On the number of non-hexagons in a planar tiling,” Comptes Rendus Mathematique, vol. 356, no. 4. Elsevier, pp. 412–414, 2018. ista: Akopyan A. 2018. On the number of non-hexagons in a planar tiling. Comptes Rendus Mathematique. 356(4), 412–414. mla: Akopyan, Arseniy. “On the Number of Non-Hexagons in a Planar Tiling.” Comptes Rendus Mathematique, vol. 356, no. 4, Elsevier, 2018, pp. 412–14, doi:10.1016/j.crma.2018.03.005. short: A. Akopyan, Comptes Rendus Mathematique 356 (2018) 412–414. date_created: 2018-12-11T11:46:19Z date_published: 2018-04-01T00:00:00Z date_updated: 2023-09-13T09:34:12Z day: '01' department: - _id: HeEd doi: 10.1016/j.crma.2018.03.005 external_id: arxiv: - '1805.01652' isi: - '000430402700009' intvolume: ' 356' isi: 1 issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1805.01652 month: '04' oa: 1 oa_version: Preprint page: 412-414 publication: Comptes Rendus Mathematique publication_identifier: issn: - 1631073X publication_status: published publisher: Elsevier publist_id: '7420' quality_controlled: '1' scopus_import: '1' status: public title: On the number of non-hexagons in a planar tiling type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 356 year: '2018' ... --- _id: '419' abstract: - lang: eng text: 'Reciprocity is a major factor in human social life and accounts for a large part of cooperation in our communities. Direct reciprocity arises when repeated interactions occur between the same individuals. The framework of iterated games formalizes this phenomenon. Despite being introduced more than five decades ago, the concept keeps offering beautiful surprises. Recent theoretical research driven by new mathematical tools has proposed a remarkable dichotomy among the crucial strategies: successful individuals either act as partners or as rivals. Rivals strive for unilateral advantages by applying selfish or extortionate strategies. Partners aim to share the payoff for mutual cooperation, but are ready to fight back when being exploited. Which of these behaviours evolves depends on the environment. Whereas small population sizes and a limited number of rounds favour rivalry, partner strategies are selected when populations are large and relationships stable. Only partners allow for evolution of cooperation, while the rivals’ attempt to put themselves first leads to defection. Hilbe et al. synthesize recent theoretical work on zero-determinant and ‘rival’ versus ‘partner’ strategies in social dilemmas. They describe the environments under which these contrasting selfish or cooperative strategies emerge in evolution.' article_processing_charge: No article_type: review author: - first_name: Christian full_name: Hilbe, Christian id: 2FDF8F3C-F248-11E8-B48F-1D18A9856A87 last_name: Hilbe orcid: 0000-0001-5116-955X - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Martin full_name: Nowak, Martin last_name: Nowak citation: ama: Hilbe C, Chatterjee K, Nowak M. Partners and rivals in direct reciprocity. Nature Human Behaviour. 2018;2:469–477. doi:10.1038/s41562-018-0320-9 apa: Hilbe, C., Chatterjee, K., & Nowak, M. (2018). Partners and rivals in direct reciprocity. Nature Human Behaviour. Nature Publishing Group. https://doi.org/10.1038/s41562-018-0320-9 chicago: Hilbe, Christian, Krishnendu Chatterjee, and Martin Nowak. “Partners and Rivals in Direct Reciprocity.” Nature Human Behaviour. Nature Publishing Group, 2018. https://doi.org/10.1038/s41562-018-0320-9. ieee: C. Hilbe, K. Chatterjee, and M. Nowak, “Partners and rivals in direct reciprocity,” Nature Human Behaviour, vol. 2. Nature Publishing Group, pp. 469–477, 2018. ista: Hilbe C, Chatterjee K, Nowak M. 2018. Partners and rivals in direct reciprocity. Nature Human Behaviour. 2, 469–477. mla: Hilbe, Christian, et al. “Partners and Rivals in Direct Reciprocity.” Nature Human Behaviour, vol. 2, Nature Publishing Group, 2018, pp. 469–477, doi:10.1038/s41562-018-0320-9. short: C. Hilbe, K. Chatterjee, M. Nowak, Nature Human Behaviour 2 (2018) 469–477. date_created: 2018-12-11T11:46:22Z date_published: 2018-03-19T00:00:00Z date_updated: 2023-09-13T09:38:54Z day: '19' ddc: - '000' department: - _id: KrCh doi: 10.1038/s41562-018-0320-9 ec_funded: 1 external_id: isi: - '000446612000016' file: - access_level: open_access checksum: 571b8cc0ba14e8d5d8b18e439a9835eb content_type: application/pdf creator: dernst date_created: 2019-11-19T08:19:51Z date_updated: 2020-07-14T12:46:25Z file_id: '7052' file_name: 2018_NatureHumanBeh_Hilbe.pdf file_size: 598033 relation: main_file file_date_updated: 2020-07-14T12:46:25Z has_accepted_license: '1' intvolume: ' 2' isi: 1 language: - iso: eng month: '03' oa: 1 oa_version: Submitted Version page: 469–477 project: - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' - _id: 2584A770-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 23499-N23 name: Modern Graph Algorithmic Techniques in Formal Verification - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: Nature Human Behaviour publication_status: published publisher: Nature Publishing Group publist_id: '7404' quality_controlled: '1' related_material: link: - relation: erratum url: http://doi.org/10.1038/s41562-018-0342-3 scopus_import: '1' status: public title: Partners and rivals in direct reciprocity type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 2 year: '2018' ... --- _id: '78' abstract: - lang: eng text: We provide a procedure for detecting the sub-segments of an incrementally observed Boolean signal ω that match a given temporal pattern ϕ. As a pattern specification language, we use timed regular expressions, a formalism well-suited for expressing properties of concurrent asynchronous behaviors embedded in metric time. We construct a timed automaton accepting the timed language denoted by ϕ and modify it slightly for the purpose of matching. We then apply zone-based reachability computation to this automaton while it reads ω, and retrieve all the matching segments from the results. Since the procedure is automaton based, it can be applied to patterns specified by other formalisms such as timed temporal logics reducible to timed automata or directly encoded as timed automata. The procedure has been implemented and its performance on synthetic examples is demonstrated. alternative_title: - LNCS article_processing_charge: No author: - first_name: Alexey full_name: Bakhirkin, Alexey last_name: Bakhirkin - first_name: Thomas full_name: Ferrere, Thomas id: 40960E6E-F248-11E8-B48F-1D18A9856A87 last_name: Ferrere orcid: 0000-0001-5199-3143 - first_name: Dejan full_name: Nickovic, Dejan last_name: Nickovic - first_name: Oded full_name: Maler, Oded last_name: Maler - first_name: Eugene full_name: Asarin, Eugene last_name: Asarin citation: ama: 'Bakhirkin A, Ferrere T, Nickovic D, Maler O, Asarin E. Online timed pattern matching using automata. In: Vol 11022. Springer; 2018:215-232. doi:10.1007/978-3-030-00151-3_13' apa: 'Bakhirkin, A., Ferrere, T., Nickovic, D., Maler, O., & Asarin, E. (2018). Online timed pattern matching using automata (Vol. 11022, pp. 215–232). Presented at the FORMATS: Formal Modeling and Analysis of Timed Systems, Bejing, China: Springer. https://doi.org/10.1007/978-3-030-00151-3_13' chicago: Bakhirkin, Alexey, Thomas Ferrere, Dejan Nickovic, Oded Maler, and Eugene Asarin. “Online Timed Pattern Matching Using Automata,” 11022:215–32. Springer, 2018. https://doi.org/10.1007/978-3-030-00151-3_13. ieee: 'A. Bakhirkin, T. Ferrere, D. Nickovic, O. Maler, and E. Asarin, “Online timed pattern matching using automata,” presented at the FORMATS: Formal Modeling and Analysis of Timed Systems, Bejing, China, 2018, vol. 11022, pp. 215–232.' ista: 'Bakhirkin A, Ferrere T, Nickovic D, Maler O, Asarin E. 2018. Online timed pattern matching using automata. FORMATS: Formal Modeling and Analysis of Timed Systems, LNCS, vol. 11022, 215–232.' mla: Bakhirkin, Alexey, et al. Online Timed Pattern Matching Using Automata. Vol. 11022, Springer, 2018, pp. 215–32, doi:10.1007/978-3-030-00151-3_13. short: A. Bakhirkin, T. Ferrere, D. Nickovic, O. Maler, E. Asarin, in:, Springer, 2018, pp. 215–232. conference: end_date: 2018-09-06 location: Bejing, China name: 'FORMATS: Formal Modeling and Analysis of Timed Systems' start_date: 2018-09-04 date_created: 2018-12-11T11:44:31Z date_published: 2018-08-26T00:00:00Z date_updated: 2023-09-13T09:35:46Z day: '26' ddc: - '000' department: - _id: ToHe doi: 10.1007/978-3-030-00151-3_13 external_id: isi: - '000884993200013' file: - access_level: open_access checksum: 436b7574934324cfa7d1d3986fddc65b content_type: application/pdf creator: dernst date_created: 2020-05-14T11:34:34Z date_updated: 2020-07-14T12:48:03Z file_id: '7831' file_name: 2018_LNCS_Bakhirkin.pdf file_size: 374851 relation: main_file file_date_updated: 2020-07-14T12:48:03Z has_accepted_license: '1' intvolume: ' 11022' isi: 1 language: - iso: eng month: '08' oa: 1 oa_version: Submitted Version page: 215 - 232 project: - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 25F42A32-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z211 name: The Wittgenstein Prize publication_identifier: isbn: - 978-3-030-00150-6 publication_status: published publisher: Springer publist_id: '7976' quality_controlled: '1' scopus_import: '1' status: public title: Online timed pattern matching using automata type: conference user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 11022 year: '2018' ... --- _id: '317' abstract: - lang: eng text: We replace the established aluminium gates for the formation of quantum dots in silicon with gates made from palladium. We study the morphology of both aluminium and palladium gates with transmission electron microscopy. The native aluminium oxide is found to be formed all around the aluminium gates, which could lead to the formation of unintentional dots. Therefore, we report on a novel fabrication route that replaces aluminium and its native oxide by palladium with atomic-layer-deposition-grown aluminium oxide. Using this approach, we show the formation of low-disorder gate-defined quantum dots, which are reproducibly fabricated. Furthermore, palladium enables us to further shrink the gate design, allowing us to perform electron transport measurements in the few-electron regime in devices comprising only two gate layers, a major technological advancement. It remains to be seen, whether the introduction of palladium gates can improve the excellent results on electron and nuclear spin qubits defined with an aluminium gate stack. article_number: '5690' article_processing_charge: No author: - first_name: Matthias full_name: Brauns, Matthias id: 33F94E3C-F248-11E8-B48F-1D18A9856A87 last_name: Brauns - first_name: Sergey full_name: Amitonov, Sergey last_name: Amitonov - first_name: Paul full_name: Spruijtenburg, Paul last_name: Spruijtenburg - first_name: Floris full_name: Zwanenburg, Floris last_name: Zwanenburg citation: ama: Brauns M, Amitonov S, Spruijtenburg P, Zwanenburg F. Palladium gates for reproducible quantum dots in silicon. Scientific Reports. 2018;8(1). doi:10.1038/s41598-018-24004-y apa: Brauns, M., Amitonov, S., Spruijtenburg, P., & Zwanenburg, F. (2018). Palladium gates for reproducible quantum dots in silicon. Scientific Reports. Nature Publishing Group. https://doi.org/10.1038/s41598-018-24004-y chicago: Brauns, Matthias, Sergey Amitonov, Paul Spruijtenburg, and Floris Zwanenburg. “Palladium Gates for Reproducible Quantum Dots in Silicon.” Scientific Reports. Nature Publishing Group, 2018. https://doi.org/10.1038/s41598-018-24004-y. ieee: M. Brauns, S. Amitonov, P. Spruijtenburg, and F. Zwanenburg, “Palladium gates for reproducible quantum dots in silicon,” Scientific Reports, vol. 8, no. 1. Nature Publishing Group, 2018. ista: Brauns M, Amitonov S, Spruijtenburg P, Zwanenburg F. 2018. Palladium gates for reproducible quantum dots in silicon. Scientific Reports. 8(1), 5690. mla: Brauns, Matthias, et al. “Palladium Gates for Reproducible Quantum Dots in Silicon.” Scientific Reports, vol. 8, no. 1, 5690, Nature Publishing Group, 2018, doi:10.1038/s41598-018-24004-y. short: M. Brauns, S. Amitonov, P. Spruijtenburg, F. Zwanenburg, Scientific Reports 8 (2018). date_created: 2018-12-11T11:45:47Z date_published: 2018-04-09T00:00:00Z date_updated: 2023-09-13T09:38:00Z day: '09' ddc: - '539' department: - _id: GeKa doi: 10.1038/s41598-018-24004-y external_id: isi: - '000429404300013' file: - access_level: open_access checksum: 20af238ca4ba6491b77270be8d826bf5 content_type: application/pdf creator: system date_created: 2018-12-12T10:17:04Z date_updated: 2020-07-14T12:46:02Z file_id: '5256' file_name: IST-2018-1016-v1+1_2018_Brauns_Palladium_gates.pdf file_size: 1850530 relation: main_file file_date_updated: 2020-07-14T12:46:02Z has_accepted_license: '1' intvolume: ' 8' isi: 1 issue: '1' language: - iso: eng month: '04' oa: 1 oa_version: Published Version publication: Scientific Reports publication_status: published publisher: Nature Publishing Group publist_id: '7548' pubrep_id: '1016' quality_controlled: '1' scopus_import: '1' status: public title: Palladium gates for reproducible quantum dots in silicon tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 8 year: '2018' ... --- _id: '194' abstract: - lang: eng text: Ants are emerging model systems to study cellular signaling because distinct castes possess different physiologic phenotypes within the same colony. Here we studied the functionality of inotocin signaling, an insect ortholog of mammalian oxytocin (OT), which was recently discovered in ants. In Lasius ants, we determined that specialization within the colony, seasonal factors, and physiologic conditions down-regulated the expression of the OT-like signaling system. Given this natural variation, we interrogated its function using RNAi knockdowns. Next-generation RNA sequencing of OT-like precursor knock-down ants highlighted its role in the regulation of genes involved in metabolism. Knock-down ants exhibited higher walking activity and increased self-grooming in the brood chamber. We propose that OT-like signaling in ants is important for regulating metabolic processes and locomotion. article_processing_charge: No article_type: original author: - first_name: Zita full_name: Liutkeviciute, Zita last_name: Liutkeviciute - first_name: Esther full_name: Gil Mansilla, Esther last_name: Gil Mansilla - first_name: Thomas full_name: Eder, Thomas last_name: Eder - first_name: Barbara E full_name: Casillas Perez, Barbara E id: 351ED2AA-F248-11E8-B48F-1D18A9856A87 last_name: Casillas Perez - first_name: Maria full_name: Giulia Di Giglio, Maria last_name: Giulia Di Giglio - first_name: Edin full_name: Muratspahić, Edin last_name: Muratspahić - first_name: Florian full_name: Grebien, Florian last_name: Grebien - first_name: Thomas full_name: Rattei, Thomas last_name: Rattei - first_name: Markus full_name: Muttenthaler, Markus last_name: Muttenthaler - first_name: Sylvia full_name: Cremer, Sylvia id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87 last_name: Cremer orcid: 0000-0002-2193-3868 - first_name: Christian full_name: Gruber, Christian last_name: Gruber citation: ama: Liutkeviciute Z, Gil Mansilla E, Eder T, et al. Oxytocin-like signaling in ants influences metabolic gene expression and locomotor activity. The FASEB Journal. 2018;32(12):6808-6821. doi:10.1096/fj.201800443 apa: Liutkeviciute, Z., Gil Mansilla, E., Eder, T., Casillas Perez, B. E., Giulia Di Giglio, M., Muratspahić, E., … Gruber, C. (2018). Oxytocin-like signaling in ants influences metabolic gene expression and locomotor activity. The FASEB Journal. FASEB. https://doi.org/10.1096/fj.201800443 chicago: Liutkeviciute, Zita, Esther Gil Mansilla, Thomas Eder, Barbara E Casillas Perez, Maria Giulia Di Giglio, Edin Muratspahić, Florian Grebien, et al. “Oxytocin-like Signaling in Ants Influences Metabolic Gene Expression and Locomotor Activity.” The FASEB Journal. FASEB, 2018. https://doi.org/10.1096/fj.201800443. ieee: Z. Liutkeviciute et al., “Oxytocin-like signaling in ants influences metabolic gene expression and locomotor activity,” The FASEB Journal, vol. 32, no. 12. FASEB, pp. 6808–6821, 2018. ista: Liutkeviciute Z, Gil Mansilla E, Eder T, Casillas Perez BE, Giulia Di Giglio M, Muratspahić E, Grebien F, Rattei T, Muttenthaler M, Cremer S, Gruber C. 2018. Oxytocin-like signaling in ants influences metabolic gene expression and locomotor activity. The FASEB Journal. 32(12), 6808–6821. mla: Liutkeviciute, Zita, et al. “Oxytocin-like Signaling in Ants Influences Metabolic Gene Expression and Locomotor Activity.” The FASEB Journal, vol. 32, no. 12, FASEB, 2018, pp. 6808–21, doi:10.1096/fj.201800443. short: Z. Liutkeviciute, E. Gil Mansilla, T. Eder, B.E. Casillas Perez, M. Giulia Di Giglio, E. Muratspahić, F. Grebien, T. Rattei, M. Muttenthaler, S. Cremer, C. Gruber, The FASEB Journal 32 (2018) 6808–6821. date_created: 2018-12-11T11:45:08Z date_published: 2018-11-29T00:00:00Z date_updated: 2023-09-13T09:37:32Z day: '29' department: - _id: SyCr doi: 10.1096/fj.201800443 external_id: isi: - '000449359700035' pmid: - '29939785' intvolume: ' 32' isi: 1 issue: '12' language: - iso: eng main_file_link: - open_access: '1' url: ' https://doi.org/10.1096/fj.201800443' month: '11' oa: 1 oa_version: Published Version page: 6808-6821 pmid: 1 project: - _id: 25E3D34E-B435-11E9-9278-68D0E5697425 name: Individual function and social role of oxytocin-like neuropeptides in ants publication: The FASEB Journal publication_identifier: issn: - '08926638' publication_status: published publisher: FASEB publist_id: '7721' quality_controlled: '1' scopus_import: '1' status: public title: Oxytocin-like signaling in ants influences metabolic gene expression and locomotor activity type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 32 year: '2018' ... --- _id: '159' abstract: - lang: eng text: L-type Ca2+ channels (LTCCs) play a crucial role in excitation-contraction coupling and release of hormones from secretory cells. They are targets of antihypertensive and antiarrhythmic drugs such as diltiazem. Here, we present a photoswitchable diltiazem, FHU-779, which can be used to reversibly block endogenous LTCCs by light. FHU-779 is as potent as diltiazem and can be used to place pancreatic β-cell function and cardiac activity under optical control. article_processing_charge: No article_type: original author: - first_name: Timm full_name: Fehrentz, Timm last_name: Fehrentz - first_name: Florian full_name: Huber, Florian last_name: Huber - first_name: Nina full_name: Hartrampf, Nina last_name: Hartrampf - first_name: Tobias full_name: Bruegmann, Tobias last_name: Bruegmann - first_name: James full_name: Frank, James last_name: Frank - first_name: Nicholas full_name: Fine, Nicholas last_name: Fine - first_name: Daniela full_name: Malan, Daniela last_name: Malan - first_name: Johann G full_name: Danzl, Johann G id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87 last_name: Danzl orcid: 0000-0001-8559-3973 - first_name: Denis full_name: Tikhonov, Denis last_name: Tikhonov - first_name: Maritn full_name: Sumser, Maritn last_name: Sumser - first_name: Philipp full_name: Sasse, Philipp last_name: Sasse - first_name: David full_name: Hodson, David last_name: Hodson - first_name: Boris full_name: Zhorov, Boris last_name: Zhorov - first_name: Nikolaj full_name: Klocker, Nikolaj last_name: Klocker - first_name: Dirk full_name: Trauner, Dirk last_name: Trauner citation: ama: Fehrentz T, Huber F, Hartrampf N, et al. Optical control of L-type Ca2+ channels using a diltiazem photoswitch. Nature Chemical Biology. 2018;14(8):764-767. doi:10.1038/s41589-018-0090-8 apa: Fehrentz, T., Huber, F., Hartrampf, N., Bruegmann, T., Frank, J., Fine, N., … Trauner, D. (2018). Optical control of L-type Ca2+ channels using a diltiazem photoswitch. Nature Chemical Biology. Nature Publishing Group. https://doi.org/10.1038/s41589-018-0090-8 chicago: Fehrentz, Timm, Florian Huber, Nina Hartrampf, Tobias Bruegmann, James Frank, Nicholas Fine, Daniela Malan, et al. “Optical Control of L-Type Ca2+ Channels Using a Diltiazem Photoswitch.” Nature Chemical Biology. Nature Publishing Group, 2018. https://doi.org/10.1038/s41589-018-0090-8. ieee: T. Fehrentz et al., “Optical control of L-type Ca2+ channels using a diltiazem photoswitch,” Nature Chemical Biology, vol. 14, no. 8. Nature Publishing Group, pp. 764–767, 2018. ista: Fehrentz T, Huber F, Hartrampf N, Bruegmann T, Frank J, Fine N, Malan D, Danzl JG, Tikhonov D, Sumser M, Sasse P, Hodson D, Zhorov B, Klocker N, Trauner D. 2018. Optical control of L-type Ca2+ channels using a diltiazem photoswitch. Nature Chemical Biology. 14(8), 764–767. mla: Fehrentz, Timm, et al. “Optical Control of L-Type Ca2+ Channels Using a Diltiazem Photoswitch.” Nature Chemical Biology, vol. 14, no. 8, Nature Publishing Group, 2018, pp. 764–67, doi:10.1038/s41589-018-0090-8. short: T. Fehrentz, F. Huber, N. Hartrampf, T. Bruegmann, J. Frank, N. Fine, D. Malan, J.G. Danzl, D. Tikhonov, M. Sumser, P. Sasse, D. Hodson, B. Zhorov, N. Klocker, D. Trauner, Nature Chemical Biology 14 (2018) 764–767. date_created: 2018-12-11T11:44:56Z date_published: 2018-07-16T00:00:00Z date_updated: 2023-09-13T09:36:35Z day: '16' ddc: - '570' department: - _id: JoDa doi: 10.1038/s41589-018-0090-8 external_id: isi: - '000438970200010' file: - access_level: open_access checksum: d42935094ec845f54a0688bf12986d62 content_type: application/pdf creator: dernst date_created: 2020-05-14T12:14:09Z date_updated: 2020-07-14T12:45:03Z file_id: '7832' file_name: 2018_NatureChemicalBiology_Fehrentz.pdf file_size: 6321000 relation: main_file file_date_updated: 2020-07-14T12:45:03Z has_accepted_license: '1' intvolume: ' 14' isi: 1 issue: '8' language: - iso: eng month: '07' oa: 1 oa_version: Submitted Version page: 764 - 767 publication: Nature Chemical Biology publication_status: published publisher: Nature Publishing Group publist_id: '7762' quality_controlled: '1' related_material: link: - relation: erratum url: https://doi.org/10.1038/s41589-021-00744-3 scopus_import: '1' status: public title: Optical control of L-type Ca2+ channels using a diltiazem photoswitch type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 14 year: '2018' ... --- _id: '79' abstract: - lang: eng text: 'Markov Decision Processes (MDPs) are a popular class of models suitable for solving control decision problems in probabilistic reactive systems. We consider parametric MDPs (pMDPs) that include parameters in some of the transition probabilities to account for stochastic uncertainties of the environment such as noise or input disturbances. We study pMDPs with reachability objectives where the parameter values are unknown and impossible to measure directly during execution, but there is a probability distribution known over the parameter values. We study for the first time computing parameter-independent strategies that are expectation optimal, i.e., optimize the expected reachability probability under the probability distribution over the parameters. We present an encoding of our problem to partially observable MDPs (POMDPs), i.e., a reduction of our problem to computing optimal strategies in POMDPs. We evaluate our method experimentally on several benchmarks: a motivating (repeated) learner model; a series of benchmarks of varying configurations of a robot moving on a grid; and a consensus protocol.' alternative_title: - LNCS article_processing_charge: No author: - first_name: Sebastian full_name: Arming, Sebastian last_name: Arming - first_name: Ezio full_name: Bartocci, Ezio last_name: Bartocci - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Joost P full_name: Katoen, Joost P id: 4524F760-F248-11E8-B48F-1D18A9856A87 last_name: Katoen - first_name: Ana full_name: Sokolova, Ana last_name: Sokolova citation: ama: 'Arming S, Bartocci E, Chatterjee K, Katoen JP, Sokolova A. Parameter-independent strategies for pMDPs via POMDPs. In: Vol 11024. Springer; 2018:53-70. doi:10.1007/978-3-319-99154-2_4' apa: 'Arming, S., Bartocci, E., Chatterjee, K., Katoen, J. P., & Sokolova, A. (2018). Parameter-independent strategies for pMDPs via POMDPs (Vol. 11024, pp. 53–70). Presented at the QEST: Quantitative Evaluation of Systems, Beijing, China: Springer. https://doi.org/10.1007/978-3-319-99154-2_4' chicago: Arming, Sebastian, Ezio Bartocci, Krishnendu Chatterjee, Joost P Katoen, and Ana Sokolova. “Parameter-Independent Strategies for PMDPs via POMDPs,” 11024:53–70. Springer, 2018. https://doi.org/10.1007/978-3-319-99154-2_4. ieee: 'S. Arming, E. Bartocci, K. Chatterjee, J. P. Katoen, and A. Sokolova, “Parameter-independent strategies for pMDPs via POMDPs,” presented at the QEST: Quantitative Evaluation of Systems, Beijing, China, 2018, vol. 11024, pp. 53–70.' ista: 'Arming S, Bartocci E, Chatterjee K, Katoen JP, Sokolova A. 2018. Parameter-independent strategies for pMDPs via POMDPs. QEST: Quantitative Evaluation of Systems, LNCS, vol. 11024, 53–70.' mla: Arming, Sebastian, et al. Parameter-Independent Strategies for PMDPs via POMDPs. Vol. 11024, Springer, 2018, pp. 53–70, doi:10.1007/978-3-319-99154-2_4. short: S. Arming, E. Bartocci, K. Chatterjee, J.P. Katoen, A. Sokolova, in:, Springer, 2018, pp. 53–70. conference: end_date: 2018-09-07 location: Beijing, China name: 'QEST: Quantitative Evaluation of Systems' start_date: 2018-09-04 date_created: 2018-12-11T11:44:31Z date_published: 2018-08-15T00:00:00Z date_updated: 2023-09-13T09:38:28Z day: '15' department: - _id: KrCh - _id: ToHe doi: 10.1007/978-3-319-99154-2_4 external_id: arxiv: - '1806.05126' isi: - '000548912200004' intvolume: ' 11024' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1806.05126 month: '08' oa: 1 oa_version: Preprint page: 53-70 publication_status: published publisher: Springer publist_id: '7975' quality_controlled: '1' scopus_import: '1' status: public title: Parameter-independent strategies for pMDPs via POMDPs type: conference user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 11024 year: '2018' ... --- _id: '400' abstract: - lang: eng text: We consider the two-dimensional BCS functional with a radial pair interaction. We show that the translational symmetry is not broken in a certain temperature interval below the critical temperature. In the case of vanishing angular momentum, our results carry over to the three-dimensional case. article_processing_charge: Yes (via OA deal) author: - first_name: Andreas full_name: Deuchert, Andreas id: 4DA65CD0-F248-11E8-B48F-1D18A9856A87 last_name: Deuchert orcid: 0000-0003-3146-6746 - first_name: Alissa full_name: Geisinge, Alissa last_name: Geisinge - first_name: Christian full_name: Hainzl, Christian last_name: Hainzl - first_name: Michael full_name: Loss, Michael last_name: Loss citation: ama: Deuchert A, Geisinge A, Hainzl C, Loss M. Persistence of translational symmetry in the BCS model with radial pair interaction. Annales Henri Poincare. 2018;19(5):1507-1527. doi:10.1007/s00023-018-0665-7 apa: Deuchert, A., Geisinge, A., Hainzl, C., & Loss, M. (2018). Persistence of translational symmetry in the BCS model with radial pair interaction. Annales Henri Poincare. Springer. https://doi.org/10.1007/s00023-018-0665-7 chicago: Deuchert, Andreas, Alissa Geisinge, Christian Hainzl, and Michael Loss. “Persistence of Translational Symmetry in the BCS Model with Radial Pair Interaction.” Annales Henri Poincare. Springer, 2018. https://doi.org/10.1007/s00023-018-0665-7. ieee: A. Deuchert, A. Geisinge, C. Hainzl, and M. Loss, “Persistence of translational symmetry in the BCS model with radial pair interaction,” Annales Henri Poincare, vol. 19, no. 5. Springer, pp. 1507–1527, 2018. ista: Deuchert A, Geisinge A, Hainzl C, Loss M. 2018. Persistence of translational symmetry in the BCS model with radial pair interaction. Annales Henri Poincare. 19(5), 1507–1527. mla: Deuchert, Andreas, et al. “Persistence of Translational Symmetry in the BCS Model with Radial Pair Interaction.” Annales Henri Poincare, vol. 19, no. 5, Springer, 2018, pp. 1507–27, doi:10.1007/s00023-018-0665-7. short: A. Deuchert, A. Geisinge, C. Hainzl, M. Loss, Annales Henri Poincare 19 (2018) 1507–1527. date_created: 2018-12-11T11:46:15Z date_published: 2018-05-01T00:00:00Z date_updated: 2023-09-15T12:04:15Z day: '01' ddc: - '510' department: - _id: RoSe doi: 10.1007/s00023-018-0665-7 ec_funded: 1 external_id: isi: - '000429799900008' file: - access_level: open_access checksum: 04d2c9bd7cbf3ca1d7acaaf4e7dca3e5 content_type: application/pdf creator: system date_created: 2018-12-12T10:12:47Z date_updated: 2020-07-14T12:46:22Z file_id: '4966' file_name: IST-2018-1011-v1+1_2018_Deuchert_Persistence.pdf file_size: 582680 relation: main_file file_date_updated: 2020-07-14T12:46:22Z has_accepted_license: '1' intvolume: ' 19' isi: 1 issue: '5' language: - iso: eng month: '05' oa: 1 oa_version: Published Version page: 1507 - 1527 project: - _id: 25C6DC12-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '694227' name: Analysis of quantum many-body systems - _id: B67AFEDC-15C9-11EA-A837-991A96BB2854 name: IST Austria Open Access Fund publication: Annales Henri Poincare publication_status: published publisher: Springer publist_id: '7429' pubrep_id: '1011' quality_controlled: '1' scopus_import: '1' status: public title: Persistence of translational symmetry in the BCS model with radial pair interaction tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 19 year: '2018' ... --- _id: '406' abstract: - lang: eng text: 'Recent developments in automated tracking allow uninterrupted, high-resolution recording of animal trajectories, sometimes coupled with the identification of stereotyped changes of body pose or other behaviors of interest. Analysis and interpretation of such data represents a challenge: the timing of animal behaviors may be stochastic and modulated by kinematic variables, by the interaction with the environment or with the conspecifics within the animal group, and dependent on internal cognitive or behavioral state of the individual. Existing models for collective motion typically fail to incorporate the discrete, stochastic, and internal-state-dependent aspects of behavior, while models focusing on individual animal behavior typically ignore the spatial aspects of the problem. Here we propose a probabilistic modeling framework to address this gap. Each animal can switch stochastically between different behavioral states, with each state resulting in a possibly different law of motion through space. Switching rates for behavioral transitions can depend in a very general way, which we seek to identify from data, on the effects of the environment as well as the interaction between the animals. We represent the switching dynamics as a Generalized Linear Model and show that: (i) forward simulation of multiple interacting animals is possible using a variant of the Gillespie’s Stochastic Simulation Algorithm; (ii) formulated properly, the maximum likelihood inference of switching rate functions is tractably solvable by gradient descent; (iii) model selection can be used to identify factors that modulate behavioral state switching and to appropriately adjust model complexity to data. To illustrate our framework, we apply it to two synthetic models of animal motion and to real zebrafish tracking data. ' acknowledgement: This work was supported by the Human Frontier Science Program RGP0065/2012 (GT, ES). article_processing_charge: Yes author: - first_name: Katarína full_name: Bod’Ová, Katarína last_name: Bod’Ová - first_name: Gabriel full_name: Mitchell, Gabriel id: 315BCD80-F248-11E8-B48F-1D18A9856A87 last_name: Mitchell - first_name: Roy full_name: Harpaz, Roy last_name: Harpaz - first_name: Elad full_name: Schneidman, Elad last_name: Schneidman - first_name: Gasper full_name: Tkacik, Gasper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkacik orcid: 0000-0002-6699-1455 citation: ama: Bod’Ová K, Mitchell G, Harpaz R, Schneidman E, Tkačik G. Probabilistic models of individual and collective animal behavior. PLoS One. 2018;13(3). doi:10.1371/journal.pone.0193049 apa: Bod’Ová, K., Mitchell, G., Harpaz, R., Schneidman, E., & Tkačik, G. (2018). Probabilistic models of individual and collective animal behavior. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0193049 chicago: Bod’Ová, Katarína, Gabriel Mitchell, Roy Harpaz, Elad Schneidman, and Gašper Tkačik. “Probabilistic Models of Individual and Collective Animal Behavior.” PLoS One. Public Library of Science, 2018. https://doi.org/10.1371/journal.pone.0193049. ieee: K. Bod’Ová, G. Mitchell, R. Harpaz, E. Schneidman, and G. Tkačik, “Probabilistic models of individual and collective animal behavior,” PLoS One, vol. 13, no. 3. Public Library of Science, 2018. ista: Bod’Ová K, Mitchell G, Harpaz R, Schneidman E, Tkačik G. 2018. Probabilistic models of individual and collective animal behavior. PLoS One. 13(3). mla: Bod’Ová, Katarína, et al. “Probabilistic Models of Individual and Collective Animal Behavior.” PLoS One, vol. 13, no. 3, Public Library of Science, 2018, doi:10.1371/journal.pone.0193049. short: K. Bod’Ová, G. Mitchell, R. Harpaz, E. Schneidman, G. Tkačik, PLoS One 13 (2018). date_created: 2018-12-11T11:46:18Z date_published: 2018-03-07T00:00:00Z date_updated: 2023-09-15T12:06:19Z day: '07' ddc: - '530' - '571' department: - _id: GaTk doi: 10.1371/journal.pone.0193049 external_id: isi: - '000426896800032' file: - access_level: open_access checksum: 684229493db75b43e98a46cd922da497 content_type: application/pdf creator: system date_created: 2018-12-12T10:15:43Z date_updated: 2020-07-14T12:46:22Z file_id: '5165' file_name: IST-2018-995-v1+1_2018_Bodova_Probabilistic.pdf file_size: 6887358 relation: main_file file_date_updated: 2020-07-14T12:46:22Z has_accepted_license: '1' intvolume: ' 13' isi: 1 issue: '3' language: - iso: eng month: '03' oa: 1 oa_version: Submitted Version project: - _id: 255008E4-B435-11E9-9278-68D0E5697425 grant_number: RGP0065/2012 name: Information processing and computation in fish groups publication: PLoS One publication_status: published publisher: Public Library of Science publist_id: '7423' pubrep_id: '995' quality_controlled: '1' related_material: record: - id: '9831' relation: research_data status: public scopus_import: '1' status: public title: Probabilistic models of individual and collective animal behavior tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 13 year: '2018' ... --- _id: '457' abstract: - lang: eng text: Temperate bacteriophages integrate in bacterial genomes as prophages and represent an important source of genetic variation for bacterial evolution, frequently transmitting fitness-augmenting genes such as toxins responsible for virulence of major pathogens. However, only a fraction of bacteriophage infections are lysogenic and lead to prophage acquisition, whereas the majority are lytic and kill the infected bacteria. Unless able to discriminate lytic from lysogenic infections, mechanisms of immunity to bacteriophages are expected to act as a double-edged sword and increase the odds of survival at the cost of depriving bacteria of potentially beneficial prophages. We show that although restriction-modification systems as mechanisms of innate immunity prevent both lytic and lysogenic infections indiscriminately in individual bacteria, they increase the number of prophage-acquiring individuals at the population level. We find that this counterintuitive result is a consequence of phage-host population dynamics, in which restriction-modification systems delay infection onset until bacteria reach densities at which the probability of lysogeny increases. These results underscore the importance of population-level dynamics as a key factor modulating costs and benefits of immunity to temperate bacteriophages article_processing_charge: No author: - first_name: Maros full_name: Pleska, Maros id: 4569785E-F248-11E8-B48F-1D18A9856A87 last_name: Pleska orcid: 0000-0001-7460-7479 - first_name: Moritz full_name: Lang, Moritz id: 29E0800A-F248-11E8-B48F-1D18A9856A87 last_name: Lang - first_name: Dominik full_name: Refardt, Dominik last_name: Refardt - first_name: Bruce full_name: Levin, Bruce last_name: Levin - first_name: Calin C full_name: Guet, Calin C id: 47F8433E-F248-11E8-B48F-1D18A9856A87 last_name: Guet orcid: 0000-0001-6220-2052 citation: ama: Pleska M, Lang M, Refardt D, Levin B, Guet CC. Phage-host population dynamics promotes prophage acquisition in bacteria with innate immunity. Nature Ecology and Evolution. 2018;2(2):359-366. doi:10.1038/s41559-017-0424-z apa: Pleska, M., Lang, M., Refardt, D., Levin, B., & Guet, C. C. (2018). Phage-host population dynamics promotes prophage acquisition in bacteria with innate immunity. Nature Ecology and Evolution. Springer Nature. https://doi.org/10.1038/s41559-017-0424-z chicago: Pleska, Maros, Moritz Lang, Dominik Refardt, Bruce Levin, and Calin C Guet. “Phage-Host Population Dynamics Promotes Prophage Acquisition in Bacteria with Innate Immunity.” Nature Ecology and Evolution. Springer Nature, 2018. https://doi.org/10.1038/s41559-017-0424-z. ieee: M. Pleska, M. Lang, D. Refardt, B. Levin, and C. C. Guet, “Phage-host population dynamics promotes prophage acquisition in bacteria with innate immunity,” Nature Ecology and Evolution, vol. 2, no. 2. Springer Nature, pp. 359–366, 2018. ista: Pleska M, Lang M, Refardt D, Levin B, Guet CC. 2018. Phage-host population dynamics promotes prophage acquisition in bacteria with innate immunity. Nature Ecology and Evolution. 2(2), 359–366. mla: Pleska, Maros, et al. “Phage-Host Population Dynamics Promotes Prophage Acquisition in Bacteria with Innate Immunity.” Nature Ecology and Evolution, vol. 2, no. 2, Springer Nature, 2018, pp. 359–66, doi:10.1038/s41559-017-0424-z. short: M. Pleska, M. Lang, D. Refardt, B. Levin, C.C. Guet, Nature Ecology and Evolution 2 (2018) 359–366. date_created: 2018-12-11T11:46:35Z date_published: 2018-02-01T00:00:00Z date_updated: 2023-09-15T12:04:57Z day: '01' department: - _id: CaGu - _id: GaTk doi: 10.1038/s41559-017-0424-z ec_funded: 1 external_id: isi: - '000426516400027' intvolume: ' 2' isi: 1 issue: '2' language: - iso: eng month: '02' oa_version: None page: 359 - 366 project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme - _id: 251BCBEC-B435-11E9-9278-68D0E5697425 grant_number: RGY0079/2011 name: Multi-Level Conflicts in Evolutionary Dynamics of Restriction-Modification Systems (HFSP Young investigators' grant) - _id: 251D65D8-B435-11E9-9278-68D0E5697425 grant_number: '24210' name: Effects of Stochasticity on the Function of Restriction-Modi cation Systems at the Single-Cell Level (DOC Fellowship) publication: Nature Ecology and Evolution publication_status: published publisher: Springer Nature publist_id: '7364' quality_controlled: '1' related_material: record: - id: '202' relation: dissertation_contains status: public scopus_import: '1' status: public title: Phage-host population dynamics promotes prophage acquisition in bacteria with innate immunity type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 2 year: '2018' ... --- _id: '55' abstract: - lang: eng text: Many animals use antimicrobials to prevent or cure disease [1,2]. For example, some animals will ingest plants with medicinal properties, both prophylactically to prevent infection and therapeutically to self-medicate when sick. Antimicrobial substances are also used as topical disinfectants, to prevent infection, protect offspring and to sanitise their surroundings [1,2]. Social insects (ants, bees, wasps and termites) build nests in environments with a high abundance and diversity of pathogenic microorganisms — such as soil and rotting wood — and colonies are often densely crowded, creating conditions that favour disease outbreaks. Consequently, social insects have evolved collective disease defences to protect their colonies from epidemics. These traits can be seen as functionally analogous to the immune system of individual organisms [3,4]. This ‘social immunity’ utilises antimicrobials to prevent and eradicate infections, and to keep the brood and nest clean. However, these antimicrobial compounds can be harmful to the insects themselves, and it is unknown how colonies prevent collateral damage when using them. Here, we demonstrate that antimicrobial acids, produced by workers to disinfect the colony, are harmful to the delicate pupal brood stage, but that the pupae are protected from the acids by the presence of a silk cocoon. Garden ants spray their nests with an antimicrobial poison to sanitize contaminated nestmates and brood. Here, Pull et al show that they also prophylactically sanitise their colonies, and that the silk cocoon serves as a barrier to protect developing pupae, thus preventing collateral damage during nest sanitation. article_processing_charge: No article_type: original author: - first_name: Christopher full_name: Pull, Christopher id: 3C7F4840-F248-11E8-B48F-1D18A9856A87 last_name: Pull orcid: 0000-0003-1122-3982 - first_name: Sina full_name: Metzler, Sina id: 48204546-F248-11E8-B48F-1D18A9856A87 last_name: Metzler orcid: 0000-0002-9547-2494 - first_name: Elisabeth full_name: Naderlinger, Elisabeth id: 31757262-F248-11E8-B48F-1D18A9856A87 last_name: Naderlinger - first_name: Sylvia full_name: Cremer, Sylvia id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87 last_name: Cremer orcid: 0000-0002-2193-3868 citation: ama: Pull C, Metzler S, Naderlinger E, Cremer S. Protection against the lethal side effects of social immunity in ants. Current Biology. 2018;28(19):R1139-R1140. doi:10.1016/j.cub.2018.08.063 apa: Pull, C., Metzler, S., Naderlinger, E., & Cremer, S. (2018). Protection against the lethal side effects of social immunity in ants. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2018.08.063 chicago: Pull, Christopher, Sina Metzler, Elisabeth Naderlinger, and Sylvia Cremer. “Protection against the Lethal Side Effects of Social Immunity in Ants.” Current Biology. Cell Press, 2018. https://doi.org/10.1016/j.cub.2018.08.063. ieee: C. Pull, S. Metzler, E. Naderlinger, and S. Cremer, “Protection against the lethal side effects of social immunity in ants,” Current Biology, vol. 28, no. 19. Cell Press, pp. R1139–R1140, 2018. ista: Pull C, Metzler S, Naderlinger E, Cremer S. 2018. Protection against the lethal side effects of social immunity in ants. Current Biology. 28(19), R1139–R1140. mla: Pull, Christopher, et al. “Protection against the Lethal Side Effects of Social Immunity in Ants.” Current Biology, vol. 28, no. 19, Cell Press, 2018, pp. R1139–40, doi:10.1016/j.cub.2018.08.063. short: C. Pull, S. Metzler, E. Naderlinger, S. Cremer, Current Biology 28 (2018) R1139–R1140. date_created: 2018-12-11T11:44:23Z date_published: 2018-10-08T00:00:00Z date_updated: 2023-09-15T12:06:46Z day: '08' department: - _id: SyCr doi: 10.1016/j.cub.2018.08.063 external_id: isi: - '000446693400008' intvolume: ' 28' isi: 1 issue: '19' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1016/j.cub.2018.08.063 month: '10' oa: 1 oa_version: Published Version page: R1139 - R1140 publication: Current Biology publication_status: published publisher: Cell Press publist_id: '7999' quality_controlled: '1' scopus_import: '1' status: public title: Protection against the lethal side effects of social immunity in ants type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 28 year: '2018' ...